Surrogate- and possibility-based design optimization for convective polymerase chain reaction devices
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TECHNICAL PAPER
Surrogate- and possibility-based design optimization for convective polymerase chain reaction devices Jung-Il Shu1 • Seong Hyeon Hong1 • Yi Wang1
•
Oktay Baysal2
Received: 5 August 2020 / Accepted: 18 August 2020 Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract This paper presents a surrogate- and possibility-based design optimization (SPBDO) methodology for robust design of convective PCR. Parametric computational fluid dynamics (CFD) models are built and simulated at sampled locations within the design space to capture the effect of design configurations on thermofluidic transport and convection–diffusionreaction in the convective PCR. A support vector machine-based classifier model is trained to retain only practically relevant data for enhanced surrogate modeling accuracy. Surrogate models are constructed by Kriging interpolation and multivariate polynomial regression methods to establish the mapping between design configurations and DNA doubling time (indicative of reactor performance). Then a process to combine the sequential method of PBDO and the surrogate model is developed, and a trade study is carried out to evaluate the impact of possibility of failure (a-value) and the balance between performance and design reliability. Our study demonstrates that the proposed SPBDO represents an effective method to consider robustness in PCR design for POC applications, especially when the uncertainty information or possibilistic characteristics of design variables is limited.
1 Introduction Polymerase chain reaction (PCR) is a novel technique that amplifies a low number of copies of deoxyribonucleic acid (DNA) to a detectable level based on thermal cyclic processes (Shu 2019; Li et al. 2016). PCR techniques have found widespread uses in a variety of biomedical and forensic applications. The cyclic processes of the PCRbased DNA amplification include denaturation, annealing, and extension. During the denaturation process, the temperature is elevated to approximately 95 C, splitting a double-stranded DNA (dsDNA) molecule into two singlestranded DNA (ssDNA) molecules (Farrar and Wittwer 2015; Muddu et al. 2011). When the temperature decreases to approximately 55 C, the annealing process initiates (Li et al. 2016), which allows primers to attach to the end of the ssDNAs, converting them into annealed DNAs (aDNA) (Li et al. 2016). During the extension process, enzymes help synthesize the aDNAs at a temperature of 72 C,
& Yi Wang [email protected] 1
University of South Carolina, Columbia, SC 29208, USA
2
Old Dominion University, Norfolk, VA 23529, USA
binding nucleotides to the tips of the primers, and hence, two aDNAs finally turn into two new dsDNAs (Shu et al. 2019a). Theoretically speaking, each thermal cycle doubles the number of copies of DNA, which are expected to increase at an exponential growth rate with the number of thermal cycles. Convective PCR uses flow convection driven by buoyancy force caused by temperature dif
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